2RKJ | pdb_00002rkj

Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P [auth N]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)
O [auth M]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)
N [auth J]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)
M [auth I]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	Nucleotidylyl transferase	8070075	3001541	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
P [auth N]	tRNA-synt_1b_1	e2rkjN1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)
O [auth M]	tRNA-synt_1b_1	e2rkjM1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)
N [auth J]	tRNA-synt_1b_1	e2rkjJ1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)
M [auth I]	tRNA-synt_1b_1	e2rkjI1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)
L [auth F]	tRNA-synt_1b_1	e2rkjF1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)
K [auth E]	tRNA-synt_1b_1	e2rkjE1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)
J [auth B]	tRNA-synt_1b_1	e2rkjB1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)
I [auth A]	tRNA-synt_1b_1	e2rkjA1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	PF00579	tRNA synthetases class I (W and Y) (tRNA-synt_1b)	tRNA synthetases class I (W and Y)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	Tyrosyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity tyrosine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding nucleic acid binding identical protein binding protein binding	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process RNA splicing regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of RNA splicing regulation of metabolic process RNA folding Group I intron splicing RNA splicing, via transesterification reactions with guanosine as nucleophile RNA splicing, via transesterification reactions mRNA processing mRNA metabolic process amino acid activation tRNA aminoacylation amino acid metabolic process tRNA metabolic process tyrosyl-tRNA aminoacylation translation tRNA aminoacylation for protein translation protein biosynthetic process protein metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
B [auth D], D [auth H], F [auth L], H [auth P]	RNA (5'-R(PGPCPUPU)-3')	-	-	-
A [auth C], C [auth G], E [auth K], G [auth O]	RNA (238-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	IPR032005	Tyrosyl-tRNA synthetase, C-terminal	Domain
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	IPR002307	Tyrosine-tRNA ligase	Family
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	IPR002305	Aminoacyl-tRNA synthetase, class Ic	Family
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	IPR024088	Tyrosine-tRNA ligase, bacterial-type	Family
I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], I [auth A], J [auth B], K [auth E], L [auth F], M [auth I], N [auth J], O [auth M], P [auth N]	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.